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The FSF holds the copyrights on many important pieces of the GNU system, such as the GCC. As a copyright holder, it has the power to enforce the GNU General Public License (GPL) when copyright infringement occurs on that software. While other copyright holders of other software systems used the GPL as their license, FSF was the only organization to regularly assert its copyright interests on software licensed under the GPL until Harald Welte created gpl-violations.org in 2004.

In late 2001, Bradley M. Kuhn (then Executive Director), with the help of Moglen, David Turner, and Peter T. Brown, turned these efforts into FSF's GPL Compliance Labs. From 2002-2004, high profile GPL enforcement cases, such as those against Linksys and OpenTV, became frequent.[1][2][3] GPL enforcement and educational campaigns on GPL compliance was a major focus of the FSF's efforts during this period.[4][5]

In March 2003, SCO filed suit against IBM alleging(saying) that IBM's contributions to some free software, including FSF's GNU, violated SCO's rights. While FSF was never a party to the lawsuit, FSF was subpoenaed on November 5, 2003.[6] During 2003 and 2004, FSF put a lot of advocacy effort into responding to the lawsuit and removing its negative impact on the adoption and promotion of free software.[7][8]

FSF sponsors a number of campaigns against what it thinks as dangers to software freedom, including software patents, digital rights management (which the FSF has called "digital restrictions management", as part of their effort to highlight their view that such technologies are "designed to take away and limit your rights,"[9]) and user interface copyright. Defective by Design is an FSF campaign against DRM. They also have a campaign to promote Ogg+Vorbis, a free alternative to proprietary formats like MP3 and AAC. They sponsor also some free software projects that are deemed to be "high-priority".

The FSF maintains a list of "high priority projects" where the Foundation says that "there is a vital need to draw the free software community's attention".[10] The FSF says these projects are"important because computer users are continually being seduced into using non-free software, because there is no adequate free replacement."